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PubMed1992

Minisatellite variant repeat (MVR) mapping: analysis of 'null' repeat units at D1S8.

Minisatellite variant repeat mapping by PCR (MVR-PCR) is a new approach to studying variation in human DNA which analyses interspersion patterns of variant repeats within minisatellite arrays. MVR-PCR has been applied to the hypervariable human minisatellite D1S8 which contains two major classes of variant 29bp repeat units designated a-type and t-type. The MVR-PCR assay uses a- or t-type specific primers, together with an amplimer at a fixed site in the DNA flanking the minisatellite, to reveal the interspersion patterns of variant repeats along an allele. Extreme levels of variation are seen both in the internal structures of individual alleles and in the digital code generated from the two superimposed alleles in total genomic DNA. However, occasional repeat units fail to amplify in MVR-PCR, signifying the existence of further repeat sequence variants termed 'null' or O-type repeats. Although not significant in individual identification, correct genotyping of null repeats is important when using MVR digital codes in parentage analysis. We have therefore characterised these null repeats and show that most null repeats share a common variant repeat sequence. We discuss the possible origins of null repeats and their application to paternity testing and the analysis of minisatellite evolution.

Alleles↗
PubMed2005

Analysis of electrophoretic patterns of arbitrarily primed PCR profiling.

We present a mathematical algorithm for the analysis of electrophoretic patterns resulting from arbitrarily primed PCR profiling. The algorithm is based on the established mathematical procedures applied to the analysis of digital images of gel patterns. The algorithm includes (a) transformation of the image into a matrix form, (b) identification of every electrophoretic lane as a set of matrix columns that are further mathematically processed, (c) averaging of matrix columns corresponding to electrophoretic lanes that define lane representatives, (d) elimination of "smiling" bands, (e) solving the problem of a lane offset, and (f) removal of the background. Representation of individual electrophoretic lanes in the form of functions allows interlane comparisons and further mathematical analysis. Direct comparison of selected lanes was obtained by employing correlation analysis. Gel images were those obtained after arbitrarily primed PCR analysis of DNA that underwent damage induced by gamma radiation from a (60)Co source. The applied method proved to be useful for elimination of subjectivity of visual inspection. It offers the possibility to avoid overlooking important differences in case of suboptimal electrophoretic resolution. In addition, higher precision is achieved in the assessment of quantitative differences due to better insight into experimental artifacts. These simple mathematical methods offer an open-type algorithm, i.e., this algorithm enables easy implementation of different parameters that may be useful for other analytical needs.

Algorithms↗
PubMed2007

BMP-7 loaded microspheres as a new delivery system for the cultivation of human chondrocytes in a collagen type-I gel.

In recent years, interest in chondrocyte cultures for transplantation has gained increasing attention. We investigated the use of PGLA microspheres as a new delivery system for BMP-7 and the effects on human chondrocytes cultivated in a 3D collagen gel culture. In an in vitro study, human chondrocytes obtained from osteoarthritic knee joints were released, transferred into a collagen type-I gel, and cultivated up to 14 days. In the treatment group PGLA microspheres loaded with human recombinant BMP-7 protein were added to the matrix. After the cultivation period, histological and immunohistochemical investigations were performed. In addition, the aggrecan core protein and type-II collagen mRNA concentrations were measured by real-time PCR. Histological staining for proteoglycan and collagen type-II protein and quantification via digital image processing revealed a significantly higher content in the samples cultivated with BMP-7 loaded microspheres in comparison to the control samples. Moreover, the collagen gel scaffold was partially remodeled by the chondrocytes and replaced by newly synthesized extracellular matrix. Cellular proliferation as well as apoptosis were low. In conclusion, we consider the PGLA microsphere system to be a functional device for the delivery of growth factors during the cultivation of articular chondrocytes leading to an increased content of type-II collagen and proteoglycan in the extracellular matrix.

Aged↗
PubMed2006

Rapid screening of fluoroquinolone resistance determinants in Streptococcus pneumoniae by PCR-restriction fragment length polymorphism and single-strand conformational polymorphism.

A rapid method, using PCR-restriction fragment length and single-strand conformation polymorphism (SSCP), was applied to screen for mutations of the fluoroquinolone resistance determinants in Streptococcus pneumoniae. One hundred nonduplicate Streptococcus pneumoniae isolates with ciprofloxacin MICs of > or = 4.0 microg/ml from the Prince of Wales Hospital, Hong Kong, years 2000 to 2003, were examined. For each isolate, PCR amplicons of quinolone resistance-determining regions (QRDRs) of gyrA, gyrB, parC, and parE genes were digested with AluI, HinfI, Sau3AI, and MspI, respectively, and analyzed by SSCP. Each SSCP pattern was given a number, and each isolate obtained a four-digit code, e.g., 1111, that represented the SSCP profile. The SSCP patterns were correlated to mutations characterized from sequence analyses of PCR amplicons. The most common SSCP profile obtained was no. 5232 (40%), which included strains with two amino acid substitutions in the ParC (Lys-137-Asn) and ParE (Ile-460-Val) genes, followed by the SSCP profile 5223 (17%), which included strains with amino acid substitutions in the ParE (Ile-460-Val) gene only. Ten isolates (10%) with amino acid substitutions at GyrA and ParE (+/-ParC) genes were resistant to levofloxacin with a MIC of > or = 16 microg/ml. Other SSCP profiles were unique in distinguishing the common amino acid substitutions in GyrA (Ser-81-Phe) and ParC (Lys-137-Asn, Ser-79-Phe plus Lys-137-Asn, Asp-83-Asn plus Lys-137-Asn, Ser-79-Phe, and Glu-96-Asp). SSCP analysis of restricted fragments generated patterns that were highly discriminative for mutations present in the QRDRs of gyrA, gyrB, parC, and parE. This method provides a database of high resolution profiles on these mutations and allows rapid screening for new mutations of the fluoroquinolone resistance genes.

Amino Acid Substitution↗
PubMed2001

Study of cytochrome P4502E1 mRNA level of mononuclear cells in patients with alcoholic liver disease.

BACKGROUND: Cytochrome P-4502E1 (CYP2E1) is an important enzyme because of its unique ability to convert many substrates to cytotoxins. The increased production of reactive intermediates by elevated enzyme concentrations leads to various pathological conditions. Therefore, it is important to detect induced CYP2E1 levels in alcoholic individuals to avoid xenobiotic-promoted liver injury. In the present investigation, we detected CYP2E1 mRNA levels of mononuclear cells obtained from 10 ml of blood by using competitive polymerase chain reaction (PCR) method. METHODS: Mononuclear cells were obtained from healthy individuals who did and did not drink habitually and patients with alcoholic liver disease (ALD). Complementary DNA synthesis was performed with RNA obtained from mononuclear cells by reverse transcription-PCR. Competitive PCR of CYP2E1 was performed with the sense (5'-CTGCAACGTCATA-GCCGACA-3') and antisense (5'-TCCATTTCCACGAGCAGGCA-3') primer and competitor DNA. Competitive PCR of beta-actin also was performed. Electrophoresis was scanned, and each band was digitized. The concentration of CYP2E1 and beta-actin mRNA was calculated from the ratio of competitor DNA. RESULTS: In healthy individuals who did and did not drink habitually, CYP2E1 mRNA levels were 103.3 copies/microl RNA and 101.7 copies/microl RNA, respectively. In actively drinking patients with ALD, CYP2E1 mRNA levels were 103.5 copies/microl RNA, but those levels decreased to 101.7 copies/microl RNA after 4 days of abstinence. No significant difference was observed in CYP2E1 mRNA levels between alcoholic fibrosis and cirrhosis. As control, we measured beta-actin mRNA levels in mononuclear cells in all samples. The mean value of beta-actin mRNA was 104.3 copies/microl RNA in all cases, which included patients with ALD. CONCLUSIONS: The results demonstrated that it is possible to measure the CYP2E1 mRNA levels of mononuclear cells in a 10 ml blood sample. The CYP2E1 mRNA level in mononuclear cells increases during drinking and decreases in abstinence for a short period of 3 to 4 days. It is concluded that CYP2E1 mRNA level may be used as an effective marker for alcoholic intake.

Actins↗
PubMed2005

Cloning and expression of equine insulin-like growth factor binding proteins in normal equine tendon.

OBJECTIVES: To define a portion of the nucleotide sequences of each of the 6 insulin-like growth factor (IGF) binding proteins (IGFBPs) in horses and describe patterns of messenger RNA (mRNA) and protein expression for IGFBPs in normal equine tendons. ANIMALS: 7 horses. PROCEDURE: Total RNA was extracted from the tensile region of normal superficial digital flexor tendons and reverse transcribed into complimentary DNA (cDNA). The cDNA was amplified via PCR, and products representing portions of each IGFBP were cloned and sequenced. Nucleotide sequences were used to deduce the amino acid sequences, and both nucleotide and predicted amino acid sequences were compared with those published for bovine, human, mouse, and ovine IGFBPs. Gene expression was quantitated by real-time PCR assay, and protein expression was evaluated by western ligand blot (WLB). RESULTS: Clones ranged in size from 262 to 522 bp and had high degrees of sequence homology with other mammalian species. Sequence homology was highest between bovine and equine IGFBPs (86% to 95%) and amongst the IGFBP-5 sequences from the various species (92% to 95%). Message for IGFBP-2 to -6, but not IGFBP-1, was expressed in normal tendon. Protein expression for IGFBP-2, -3, and -4 was detected byWLB in normal tendon and markedly increased in damaged tendons. CONCLUSIONS AND CLINICAL RELEVANCE: Results provide basic information and tools needed for further characterization of the role of the IGF system in tendon healing and may lead to the ability to potentiate the response of healing tendon to exogenous IGF-I via concurrent manipulation of IGFBPs.

Amino Acid Sequence↗
PubMed2003

[Acute pharmacologic poisoning (I). Psychotropic and antiarrhythmic drugs].

In the evaluation of Acute Drug Poisoning (ADP) in patients seriously ill with a potentially non-toxic dose of the drug that is theoretically responsible, it is important to insist on anamnesis in the coingestion of other drugs or toxics. Initially attention is given to life support measures, oxygenation, protection of the airway and expanding the volemia. The ECG is a diagnostic tool of the first order in ADPs, above all for tricyclic antidepressants (TAD) and cardio-vascular drugs. In the majority of cases continuous monitoring is usually necessary during the first 12-24 hours. The benzodiazepines do not usually give rise to serious poisoning. The use of flumazenil will be reserved for cases of respiratory depression, deep coma or where the cause is undetermined. They can give rise to convulsions, above all in the case of mixed poisonings with anti-depressants and abstinence syndrome. The TADs have an enormous potential seriousness, as they can cause mortal arrhythmias. The therapeutic range of lithium is very narrow; it can produce signs of basically digestive and neurological toxicity. In the case of poisoning by digoxin, the use of anti-digital anti-bodies will be considered in cases of serious bradyarrhythmias, AV blocks or PCR. Glucagon is the antidote for serious poisoning by beta-blockers and for refractory hypotension in cases of calcioantagonists.

Acute Disease↗
PubMed1996

Retinal Thy-1 expression during development.

PURPOSE: To evaluate the developmental expression of Thy-1 in the retina. Thy-1, the most abundant mammalian neuronal surface glycoprotein, is likely to play a significant role in retinal development. In the mammalian retina, it is found predominantly, if not exclusively, on retinal ganglion cells. METHODS: Rat retinae of various ages were stained immunohistochemically for Thy-1 with 2G12, a monoclonal Thy-1 antibody. Sections were analyzed digitally to quantify bound antibody. Using semiquantitative reverse transcription-polymerase chain reaction (RT-PCR), the expression of Thy-1 protein was compared with the levels of mRNA detected. RESULTS: Thy-1-dependent fluorescence was detected in rat retinae from birth, albeit at low levels. Thy-1 labeling was localized predominantly to the ganglion cell layer. Minimal, fine patterns of linear and reticular fluorescence were noted in the inner nuclear layer. Thy-1 levels reached a maximal level at approximately postnatal day 14. RT-PCR measurements showed a similar time course for the increase in Thy-1 expression. CONCLUSIONS: The Thy-1 antigen is present in the inner retina at birth. Its level increases steadily after birth and peaks during the second week of life. Thy-1 expression is approximately coterminous with synaptogenesis of the inner plexiform layer and may play a role in synaptogenesis of the inner retina or in other developmental milestones in the formation of the visual system.

Animals↗
PubMed2007

Quantitation of Guggenheimella bovis and treponemes in bovine tissues related to digital dermatitis.

Digital dermatitis is an inflammation of uncertain aetiology in the skin of the foot of cattle. In 2005, a novel microorganism, Guggenheimella bovis, was isolated from the advancing front of digital dermatitis lesions, suggesting a possible role in pathogenesis. In the present study, tissue samples of 20 affected cows were examined by quantitative PCR for G. bovis, treponemes and the total eubacterial load. High numbers of eubacteria and treponemes were found in most lesions, whereas only a few lesions contained Guggenheimella, and only at low concentrations. The results argue against the relevance of G. bovis in the aetiology of digital dermatitis in cattle, but are consistent with a role for treponemes.

Animals↗
PubMed1996

A quantitative method of determining initial amounts of DNA by polymerase chain reaction cycle titration using digital imaging and a novel DNA stain.

A new nonradioactive method is described for quantitative determination of small amounts of DNA by PCR, examplified with mitochondrial DNA. The method represents a combination of serial dilution PCR and kinetic PCR and avoids the use of radioactivity by applying the fluorescent dye SYBR Green I, allowing visualization of PCR amplified bands on agarose gels in a broad exponential range of PCR cycles. After recording agarose gel images with a video camera in a computer, the band intensities are processed with the NIH image program and analyzed by a new graphical method. This nonradioactive method allows calculation of small original amounts of specific DNA in samples at high accuracy.

Base Sequence↗
PubMed2000

A spirochete isolated from a case of severe virulent ovine foot disease is closely related to a Treponeme isolated from human periodontitis and bovine digital dermatitis.

The isolation of spirochetes from severe ovine foot disease has been reported recently by our research group. In this study we describe the preliminary classification of this spirochete based on nucleotide sequence analysis of the PCR-amplified 16S rRNA gene. Phylogenetic analysis of this sequence in comparison with other previously reported 16S rRNA gene sequences showed that the spirochete belonged to the treponemal phylotype Treponema vincentii which has been associated with bovine digital dermatitis and human periodontal disease. Further work is required to define the common virulence determinants of these closely related treponemes in the aetiology of these tissue destructive diseases.

Animals↗
PubMedDate not supplied

[The use of computer morphodensitometry in modern molecular diagnostic methods].

Technologies based on the use of polymerase chain reaction, in particular IS PCR are widely used now. However, wide introduction in clinico-laboratory practice of these methods requires: increase of reliability of the accepted decisions, improvement of the image for revealing more fine distinctions of objects, increase of quality of the obtained information, automated registration of results of the analysis. The application of original digital image analysis, adapted to specificity of biomedical objects--morphodensitometry--allows to solve successfully the following tasks: to optimisze conditions of IS PCR realisation on the basis of use of quantitative opticogeometrical parameters, quantitatively and subpopulistically to characterize a degree of infected cells with viral infection, and also nucleuses of cells, that is especially actual for introduction of molecular-genetic methods in clinico diagnostic practice and, automatically to register results of the analysis. Thus, employment of morphodensitometry can be very important in genediagnostic and also gene therapy.

Animals↗
PubMed1998

The frequent detection of a treponeme in bovine digital dermatitis by immunocytochemistry and polymerase chain reaction.

A study was carried out to determine whether spirochaetes are frequently associated with digital dermatitis in United Kingdom (UK) dairy cattle. Histopathological examination of lesions using a silver stain showed a large number of unidentified spirochaete-like organisms present in digital dermatitis hoof skin tissue in all examined biopsies. Immunocytochemical staining demonstrated that spirochaetes in skin lesions were identified by polyclonal antisera to Borrelia burgdorferi, Treponema denticola and Treponema vincentii (again all biopsies were positively stained), whereas monoclonal antibodies to B. burgdorferi and any Treponema pallidum did not stain any organisms in all biopsies. A PCR of 16S rRNA, previously shown to be specific for a new treponeme, was employed and produced positive results from 82.4% of digital dermatitis tissues. It is concluded that this spirochaete (or related spirochaetes), which is similar to human oral treponemes, is frequently associated with, and may be responsible for, pathological changes in digital dermatitis.

Animals↗
PubMed1995

Enhanced reverse transcriptase-polymerase chain reaction for prostate specific antigen as an indicator of true pathologic stage in patients with prostate cancer.

BACKGROUND: As up to 50% of all patients with prostate cancer who have undergone radical prostatectomy are found to be understaged subsequent to surgery, a more sensitive early staging modality currently is needed. A molecular assay that detects prostate specific antigen (PSA)-synthesizing cells in the peripheral circulation of patients with prostate cancer is described. METHODS: An enhanced reverse-transcriptase polymerase chain reaction (RT-PCR) assay specific for PSA mRNA was performed on RNA extracted from blood drawn from 94 patients before radical prostatectomy. Surgical specimens were examined to determine the extent of tumor spread. The assay was compared with imaging modalities, digital rectal examination, and serum PSA level as predictors of pathology. Additionally, patients were monitored postoperatively by serum PSA level to determine any potential correlation between patient RT-PCR scores and subsequent tumor recurrence. RESULTS: Postoperative pathology revealed that 36 of the 94 patients had extraprostatic disease at the time of surgery. Enhanced RT-PCR identified 26 of these patients from preoperative blood specimens (72% sensitivity). The test was negative for 51 of the 58 patients with organ-confined disease (88% specificity). An odds ratio analysis showed that no other preoperative staging modality was related more strongly to extraprostatic or organ-confined disease. Follow-up PSA determinations revealed that RT-PCR positive patients were at higher risk for a recurrence. At 6 months after surgery, the rates for an increased PSA were 19 and 2% for RT-PCR-positive and -negative patients, respectively. CONCLUSIONS: The data from this follow-up study continue to support the utility of enhanced RT-PCR as an early staging modality for radical prostatectomy candidates.

Androgen Antagonists↗
PubMed2003

[A new method of processing quantitative PCR data].

Today standard PCR can't satisfy the need of biotechnique development and clinical research any more. After numerous dynamic research, PE company found there is a linear relation between initial template number and cycling time when the accumulating fluorescent product is detectable.Therefore,they developed a quantitative PCR technique to be used in PE7700 and PE5700. But the error of this technique is too great to satisfy the need of biotechnique development and clinical research. A better quantitative PCR technique is needed. The mathematical model submitted here is combined with the achievement of relative science,and based on the PCR principle and careful analysis of molecular relationship of main members in PCR reaction system. This model describes the function relation between product quantity or fluorescence intensity and initial template number and other reaction conditions, and can reflect the accumulating rule of PCR product molecule accurately. Accurate quantitative PCR analysis can be made use this function relation. Accumulated PCR product quantity can be obtained from initial template number. Using this model to do quantitative PCR analysis,result error is only related to the accuracy of fluorescence intensity or the instrument used. For an example, when the fluorescence intensity is accurate to 6 digits and the template size is between 100 to 1,000,000, the quantitative result accuracy will be more than 99%. The difference of result error is distinct using same condition,same instrument but different analysis method. Moreover,if the PCR quantitative analysis system is used to process data, it will get result 80 times of accuracy than using CT method.

English Abstract↗
PubMed1998

Cyclooxygenase isoenzyme localization and mRNA expression in rat lungs.

Prostanoid generation may proceed via both isoforms of cyclooxygenase, Cox-1 and Cox-2. Cox-1 is thought to be ubiquitously expressed, whereas Cox-2 is mostly assumed to be dynamically regulated, responding to inflammatory stimuli. The cellular localization of Cox-1 and Cox-2 in the lung, an organ with high cyclooxygenase activity, is not known. In normal rat lungs the expression and localization of Cox-1 and Cox-2 were examined with immunogold-silver staining and the RT-PCR technique. Quantitative image analysis of the staining intensity was performed by measuring mean gray values of digitized epipolarization images. Expression of both Cox-1 and Cox-2 was readily detectable in rat lungs. Cox-1 immunoreactivity localized predominantly to bronchial epithelial cells, smooth muscle cells of large hilum veins, and (with lower expression) to alveolar macrophages and pulmonary artery endothelial cells. The most intense Cox-2 staining was noted in macrophage- and mast cell-like cells, detected in close vicinity to the bronchial epithelium and in the connective tissue surrounding the vessels. In addition, strong Cox-2 expression was found in smooth muscle cells of partially muscular vessels and large veins of the hilum. Bronchial epithelial cells displayed Cox-2 immunoreactivity with limited intensity. Alveolar macrophages and alveolar septal cells were only occasionally stained with anti-Cox-2 antibodies. Both Cox-1 and Cox-2 are constitutively expressed in several cell types of normal rat lung, but display clearly different patterns of cellular localization. Cox-2 may not be related only to lung inflammation, but is suggested to be implicated in regulatory processes under physiological conditions as well.

Animals↗
PubMed2006

Thyroxine affects expression of KSPG-related genes, the carbonic anhydrase II gene, and KS sulfation in the embryonic chicken cornea.

PURPOSE: Opaque chick corneas become thin and transparent from embryonic day (E)9 to E20 of incubation. Thyroxine (T4) injected in ovo on E9 induces precocious transparency by E12. The present study was conducted to determine whether corneal cells differentially express genes for T4 regulation, keratan sulfate proteoglycan (KSPG) synthesis, crystallins, and endothelial cell ion transporters during transparency development and whether these expressions are altered when E9 embryos are treated with T4. METHODS: E9 eggs received T4 or buffer; corneas were dissected on E12. Corneal transparency was measured digitally and thickness was determined from cryostat cross sections. mRNA expressions were determined by real-time PCR using cDNA synthesized from whole-cell RNA, cells expressing T4 receptor mRNAs assessed by in situ hybridization, and KS disaccharide sulfation measured by electrospray ionization tandem mass spectrometry (ESI-MS/MS). RESULTS: All corneal layers expressed T4 receptor alpha (THRA) mRNA; keratocytes and endothelial cells expressed T4 receptor beta (THRB) mRNA. During normal development, THRB expression increased 20-fold from E12 to E20; THRA expression remained constant. Expressions of most genes involved in KS synthesis increased from E9 to E16, and then decreased from E16 to E20. From E9 to E20, expressions of crystallin genes increased; T4/3-deiodinase DIII (DIO3) increased 10-fold; and sodium-potassium ATPase transporter (ATP1A1), sodium-bicarbonate transporter (NBC), and carbonic anhydrase II (CA2) increased 5- to 10-fold. E9 T4 administration decreased corneal thickness by E12; increased DIO3, THRB, and CA2 expressions 5- to 20-fold; decreased KSPG core protein genes and galactose sulfotransferase CHST1 expressions 2-fold; and reduced KS disulfated/monosulfated disaccharide (DSD/MSD) ratios. CONCLUSIONS: Thyroxine modifies expressions of KSPG synthesis and carbonic anhydrase genes.

Animals↗
PubMed2001

Beta-2 adrenergic receptor gene variations and blood pressure under stress in normal twins.

We tested the hypothesis that blood pressure (BP) responses to physical and mental stress are associated with polymorphisms in the beta-2 adrenergic receptor (AR) gene. We studied normotensive, young, monozygotic (MZ) and dizygotic (DZ) twins. The subjects underwent automated BP measurements at the brachial and digital arteries and were subjected to mental arithmetic and cold pressor stress. We used allele-specific PCR to genotype four single nucleotide polymorphisms in the beta-2 AR gene. The most functionally relevant polymorphism in the beta-2 AR gene, Arg16/Gly, was associated with systolic and diastolic BP under resting conditions, during mental arithmetic, and during the cold pressor test, as well as with the increase in diastolic BP during both forms of stress. These findings support a role for the beta-2 AR gene in BP regulation. They also indicate that the beta-2 AR gene influences the level of not only resting but also stress-related BP.

Blood Pressure↗